Single nucleotide polymorphism screening and bioinformatics analysis of TBC1D7 gene in Guanling cattle

doi:10.3969/j.issn.1004-1524.2022.07.07

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (7): 1402-1411.DOI: 10.3969/j.issn.1004-1524.2022.07.07

• Animal Science • Previous Articles Next Articles

Single nucleotide polymorphism screening and bioinformatics analysis of TBC1D7 gene in Guanling cattle

LIU Pengcheng¹(), ZHANG Ji¹, QIU Ganyuan¹, GONG Yu², LI Xuesong², LI Wei², ZHANG Yiyu¹, LIU Ruoyu¹^,^*()

1. Key Laboratory of Plateau and Mountain Animal Genetics and Breeding, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
2. Guizhou Province Livestock and Poultry Genetic Resources Management Station, Guiyang 550001, China

Received:2020-11-17 Online:2022-07-25 Published:2022-07-26
Contact: LIU Ruoyu

Abstract

Abstract:

In order to explore effects of single nucleotide polymorphism(SNPs)of TBC1 domain family,member 7(TBC1D7)gene on cattle growth traits, the Guizhou Guanling cattle was selected as experimental objects to construct DNA pools. After PCR amplification, direct sequencing method was used to detect SNPs of TBC1D7 gene in Guanling cattle. The results showed that the coding region of TBC1D7 gene of Guanling cattle was 882 bp in length, encoding 293 amino acids. An unstable soluble protein was formed. There was no transmembrane region and no signal peptide in the protein encoded by TBC1D7 gene, which is a non-secretory protein. There were six potential N-glycosylation sites in the protein, and the secondary structure was mainly composed of α-helix and random coil. Four synonymous mutation sites were found in the coding sequence (CDS) region of TBC1D7 gene in Guanling cattle, namely, c.402T>C, c.414A>G, c.609C>T and c.648T>C. All the four SNPs resulted in changes in mRNA secondary structure, free energy and gene frequency of TBC1D7 gene in Guanling cattle. In this study, four SNPs loci of TBC1D7 gene in Guanling cattle were screened. The results showed that the polymorphism of TBC1D7 gene in Guanling cattle was abundant, which provided a theoretical basis for further research on the correlation between the variation of TBC1D7 gene and the growth and development traits of Guanling cattle.

Key words: Guanling cattle, TBC1D7 gene, single nucleotide polymorphism, bioinformatics

CLC Number:

S834.89

LIU Pengcheng, ZHANG Ji, QIU Ganyuan, GONG Yu, LI Xuesong, LI Wei, ZHANG Yiyu, LIU Ruoyu. Single nucleotide polymorphism screening and bioinformatics analysis of TBC1D7 gene in Guanling cattle[J]. Acta Agriculturae Zhejiangensis, 2022, 34(7): 1402-1411.

Figures/Tables 14

References 20

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引物名称 Primer name	上游引物 Forward primer (5'→3')	下游引物 Reverse primer(5'→3')	产物长度 Product length/bp	退火温度 Annealing temperature/ ℃	扩增区域 Amplified region
P1	CCCTGACGCCGAGGTAAC	CGTCCTCCAGGAAGAAATCA	397	56	3'UTR-Exon1-Intron1
P2	TGGCGAAAATCACGGAAT	TCTGGGATGACTGAGAACCA	248	58	Intron1-Exon2-Intron2
P3	TCACGATCAGCATGAAAAGC	ACCAATGACCCCATCAATTT	197	58	Intron1-Exon3-Intron2
P4	CCCACCCCGGGTCTCTAT	AGAGTCAAGCCAAGGGTCAA	245	60	Intron1-Exon4-Intron2
P5	TCTCTTGCCTCCTTGAGTTG	TGGTAAGGGCATTTCCTCAG	250	54	Intron1-Exon5-Intron2
P6	TGAGTAATCTCTTCCCCTTCAATC	CAGGATTTTTCTGACTCTGTGC	226	54	Intron1-Exon6-Intron2
P7	TTTGAAACTTGAGCTGTTTAGGTG	TTCAAGTGAAGCAAAGCACA	227	58	Intron1-Exon7-Intron2
P8.1	TTTCAGAGCCTGGTCTGCTT	CCACCCTGCATCTAATGACC	938	62	Intron7-Exon8-5'UTR
P8.2	GGACTTGATGCTTTGCTGAA	GTATGGCATTTGGGATGGAC	783	58	Intron7-Exon8-5'UTR
P8.3	AGGTCCTTGTTGGTCATCCA	TTCTGGAGCCAGGACTCACT	478	62	Intron7-Exon8-5'UTR

引物名称 Primer name	上游引物 Forward primer (5'→3')	下游引物 Reverse primer(5'→3')	产物长度 Product length/bp	退火温度 Annealing temperature/ ℃	扩增区域 Amplified region
P1	CCCTGACGCCGAGGTAAC	CGTCCTCCAGGAAGAAATCA	397	56	3'UTR-Exon1-Intron1
P2	TGGCGAAAATCACGGAAT	TCTGGGATGACTGAGAACCA	248	58	Intron1-Exon2-Intron2
P3	TCACGATCAGCATGAAAAGC	ACCAATGACCCCATCAATTT	197	58	Intron1-Exon3-Intron2
P4	CCCACCCCGGGTCTCTAT	AGAGTCAAGCCAAGGGTCAA	245	60	Intron1-Exon4-Intron2
P5	TCTCTTGCCTCCTTGAGTTG	TGGTAAGGGCATTTCCTCAG	250	54	Intron1-Exon5-Intron2
P6	TGAGTAATCTCTTCCCCTTCAATC	CAGGATTTTTCTGACTCTGTGC	226	54	Intron1-Exon6-Intron2
P7	TTTGAAACTTGAGCTGTTTAGGTG	TTCAAGTGAAGCAAAGCACA	227	58	Intron1-Exon7-Intron2
P8.1	TTTCAGAGCCTGGTCTGCTT	CCACCCTGCATCTAATGACC	938	62	Intron7-Exon8-5'UTR
P8.2	GGACTTGATGCTTTGCTGAA	GTATGGCATTTGGGATGGAC	783	58	Intron7-Exon8-5'UTR
P8.3	AGGTCCTTGTTGGTCATCCA	TTCTGGAGCCAGGACTCACT	478	62	Intron7-Exon8-5'UTR

突变位点 Mutation site	等位基因频率Allele frequency
突变位点 Mutation site	突变前Before mutation	突变后After mutation
c.402T>C	0.609 2	0.390 8
c.414A>G	0.607 1	0.392 9
c.609C>T	0.5254	0.474 6
c.648T>C	0.523 8	0.476 2

突变位点 Mutation site	等位基因频率Allele frequency
突变位点 Mutation site	突变前Before mutation	突变后After mutation
c.402T>C	0.609 2	0.390 8
c.414A>G	0.607 1	0.392 9
c.609C>T	0.5254	0.474 6
c.648T>C	0.523 8	0.476 2

氨基酸 Amino acid	数量 Number	比例 Frequency/%	氨基酸 Amino acid	数量 Number	比例 Frequency/%
Ala	16	5.5	Leu	35	11.9
Arg	14	4.8	Lys	23	7.8
Asn	6	2.0	Met	8	2.7
Asp	15	5.1	Phe	14	4.8
Cys	9	3.1	Pro	15	5.1
Gln	10	3.4	Ser	26	8.9
Glu	23	7.8	Thr	9	3.1
Gly	7	2.4	Trp	5	1.7
His	9	3.1	Tyr	11	3.8
Ile	14	4.8	Val	24	8.2

Single nucleotide polymorphism screening and bioinformatics analysis of TBC1D7 gene in Guanling cattle

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